We have developed a method of generating ab initio the effective Hamiltonian for the valence electrons in a large molecule. The effective Hamiltonian operates in the finite dimensional Hilbert space spanned by antisymmetrized products of valence orbitals. The procedure is based on a cluster expansion of the canonically transformed Hamiltonian in which the transformation eliminates the interaction with core electrons and builds in correlation effects among the valence electrons. The goal of this research is the construction ab initio of valence electron Hamiltonians for systems such as the pi electrons of the DNA based and visual chromophores. In addition, we want to justify the use of semi- empirical theories and in so doing predict their parameters from a first principles calculation. Currently the computer codes for the numerical implication of the formalism are being written and tested on small systems such as ethylene, benzene, and the peptide linkage. Calculations of the electric-dipole transition probabilities using the canonically transformed momentum and length operators are envisioned.